Dorothy,
San Francisco is on a long peninsula between the San Francisco Bay and the Pacific Ocean. The only railroad connection into San Francisco is from the south. Historically, trains ran from San Francisco south to San Jose and Los Angeles (and CalTrans wants to bring inter-city service to this line again in the future). Today, this line is served by Caltrain commuter trains between San Jose and San Francisco. Anyway, since the
Coast Starlight comes and goes from the north, it can't get into San Francisco directly.
There is a bus from the Emeryville station that is dedicated for Amtrak passengers. It connects with the train (and waits for it if it's late). There are other options for crossing the Bay, too. One of San Francisco's subways (BART) has a line crossing the bay, and trains are fast and frequent. Unfortunately, none of the BART stations are directly adjacent to places where the
Coast Starlight stops. There are also ferry connections.
Emeryville may not be in San Francisco, but it's part of an integrated region. I suppose the best analogy would be to an airport. Most of those aren't directly in the city, either. At least with Amtrak, they give you a direct bus ride across the Bay Bridge. And Emeryville is probably closer to Downtown San Francisco than most airports are to their city-center.
The West Coast:
As for touring the west coast, you will be treated to some spectacular scenery.
Seattle is one of my favorite American cities. There's lots to see and do, and the locals are very friendly. The city is in a beautiful setting, too, with water on both sides of Downtown and distant mountains visible to the east and west. And of course, the massive Mount Rainier lurks to the south.
If you're going to
Portland, keep in mind that it's not a huge, cosmopolitan place. There is plenty to do there, of course. But if all you've got is 2 hours in the city, all you're probably going to have time to see is the train station, and maybe ride the light rail (tram) through Downtown and back. Spending a day or two would give you a lot more time to see things.
There's only one daily train in each direction between Portland and Sacramento, the
Coast Starlight. You will go through some very mountainous areas, but depending on what time of year, a lot of the scenery will be after dark. In the summer, the light lasts longer.
The capital of the state of California is
Sacramento. There is frequent Amtrak service between Sacramento and the Bay Area (San Francisco). I don't know how much time you have to play around with, but Sacramento is the kind of place where you could easily spend just 3 or 4 hours. The California State Railroad Museum is just a few blocks from the Amtrak station, and it's a very good railroad museum.
The
San Francisco Bay Area is a very cool place. You could spend a week there and not see half of what the city has to offer. Sounds like this is already on your agenda.
The ride down to Los Angeles will be along the Pacific coast once you pass San Luis Obispo. I haven't taken this part of the trip (but I'm doing it in June), and I've heard that it's spectacular.
You get into
Los Angeles late in the evening. LA is also a place with much to do. I've been three times, and haven't even scratched the surface. You'll definitely want to schedule some time there. I highly recommend a trip to the Griffith Observatory. It's in the Hollywood Hills above the LA Basin, and the whole city is laid out in front of you. There's an LADOT bus that operates every 35 minutes on Saturday and Sunday from the Vermont/Sunset Metro station to the Observatory.
Here's a
pic I took from the top in October. Definitely a must-see if you're going to be in LA:
"Observing Los Angeles" by
tracktwentynine on Flickr.
Las Vegas has not been served by Amtrak since 1997.
Note, Las Vegas, NEW MEXICO is served by Amtrak, but that is not the famous city. It's just a small town with no casinos. I've never been, so I can't make any recommendations.
However, you might want to consider visiting
San Diego, instead. It's a beautiful city with an amazing climate. The San Diego Zoo is world renown. Amtrak runs trains about every 90 minutes between LA and San Diego, and they also run right along the beach, making for some fantastic views along the way.
And one other thing to consider. I don't know if you're interested in visiting Canada, but
Vancouver is a great city. I like it even more than Seattle. There are two Amtrak trains a day in each direction between Vancouver and Seattle, so it could be on your rail tour.
Good luck and happy travels!